Variant report

Variant	rs11650283
Chromosome Location	chr17:16239832-16239833
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16117546..16120375-chr17:16238213..16240874,2	MCF-7	breast:
2	chr17:16230260..16232698-chr17:16238773..16240667,2	K562	blood:

Variant related genes	Relation type
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10852834	0.82[ASN][1000 genomes]
rs11650427	0.83[TSI][hapmap]
rs11650956	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11651578	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11651955	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11653585	0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11654658	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11655906	0.87[EUR][1000 genomes]
rs11655907	0.87[EUR][1000 genomes]
rs11656811	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11868284	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12449629	0.84[EUR][1000 genomes]
rs12936233	0.83[TSI][hapmap]
rs12936529	0.82[ASN][1000 genomes]
rs12938397	0.85[TSI][hapmap]
rs12938878	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12939078	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12945855	0.83[TSI][hapmap]
rs12945877	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946717	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12947973	0.83[EUR][1000 genomes]
rs12948680	0.84[EUR][1000 genomes]
rs12948905	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12949255	0.81[EUR][1000 genomes]
rs12949537	0.80[EUR][1000 genomes]
rs1476810	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs15739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16959630	0.95[CHD][hapmap];0.88[JPT][hapmap]
rs1963811	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2014604	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap]
rs2109262	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2324306	0.86[ASN][1000 genomes]
rs2324307	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28862997	0.82[EUR][1000 genomes]
rs3112511	0.82[CEU][hapmap];0.83[GIH][hapmap]
rs3112513	0.82[CEU][hapmap];0.83[GIH][hapmap]
rs35762856	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3785620	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3785621	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap]
rs3785622	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3785623	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap]
rs3785625	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3785626	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4791665	0.81[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap]
rs4792728	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4792729	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4792731	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4792732	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4792735	0.87[EUR][1000 genomes]
rs56326304	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56952590	0.81[ASN][1000 genomes]
rs62074191	0.88[ASN][1000 genomes]
rs62074192	0.88[ASN][1000 genomes]
rs6502498	0.86[ASN][1000 genomes]
rs6502499	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs7210990	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7219687	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap]
rs7224367	0.81[EUR][1000 genomes]
rs7477	0.89[TSI][hapmap]
rs8074246	0.88[ASN][1000 genomes]
rs8074727	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9747806	0.87[ASN][1000 genomes]
rs9890539	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs9890867	0.92[EUR][1000 genomes]
rs9893005	0.82[EUR][1000 genomes]
rs9907261	0.81[ASN][1000 genomes]
rs9910148	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9914734	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9944524	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
6	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11650283	TRPV2	cis	cerebellum	SCAN
rs11650283	PRPSAP2	cis	parietal	SCAN
rs11650283	CENPV	cis	Artery Tibial	GTEx
rs11650283	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs11650283	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs11650283	ADORA2B	cis	Muscle Skeletal	GTEx
rs11650283	TRPV2	cis	parietal	SCAN
rs11650283	ZSWIM7	cis	Muscle Skeletal	GTEx
rs11650283	ELAC2	cis	parietal	SCAN
rs11650283	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs11650283	CENPV	cis	parietal	SCAN
rs11650283	ADORA2B	cis	Artery Tibial	GTEx
rs11650283	PRR6	cis	multi-tissue	Pritchard
rs11650283	CENPV	cis	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16201600-16246400	Weak transcription	Fetal Brain Male	brain
2	chr17:16205800-16245600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:16206000-16245800	Weak transcription	Brain Anterior Caudate	brain
4	chr17:16206000-16246000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr17:16209000-16245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr17:16214600-16255200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:16217000-16246000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:16217200-16255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr17:16219200-16246000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:16222800-16245600	Weak transcription	Right Ventricle	heart
11	chr17:16225800-16245800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr17:16226600-16245600	Weak transcription	Fetal Kidney	kidney
13	chr17:16229400-16255600	Weak transcription	Esophagus	oesophagus
14	chr17:16230200-16246000	Weak transcription	Spleen	Spleen
15	chr17:16230400-16245600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:16230400-16245600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr17:16230400-16245600	Weak transcription	Brain Germinal Matrix	brain
18	chr17:16230400-16245600	Weak transcription	Placenta	Placenta
19	chr17:16230400-16246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:16230400-16246200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:16230400-16253600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:16230400-16255000	Weak transcription	Primary B cells from cord blood	blood
23	chr17:16230400-16255200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr17:16230400-16255200	Weak transcription	Brain Substantia Nigra	brain
25	chr17:16230600-16243800	Weak transcription	Thymus	Thymus
26	chr17:16230600-16244000	Weak transcription	Primary T cells from cord blood	blood
27	chr17:16230600-16245400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr17:16230600-16245600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:16230600-16245600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr17:16230600-16245600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr17:16230600-16245600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr17:16230600-16245600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr17:16230600-16245600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr17:16230600-16245600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:16230600-16245600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr17:16230600-16245600	Weak transcription	Fetal Thymus	thymus
37	chr17:16230600-16245600	Weak transcription	Left Ventricle	heart
38	chr17:16230600-16245800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr17:16230600-16245800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr17:16230600-16245800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr17:16230600-16245800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr17:16230600-16245800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr17:16230600-16246000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr17:16230600-16246000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr17:16230600-16246000	Weak transcription	Brain Hippocampus Middle	brain
46	chr17:16230600-16246000	Weak transcription	Dnd41	blood
47	chr17:16230600-16246400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr17:16230600-16250800	Weak transcription	Brain Angular Gyrus	brain
49	chr17:16230600-16254200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr17:16230600-16255200	Weak transcription	Colon Smooth Muscle	Colon

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